Does anyone have a favorite splice site prediction / evaluation tool? (This would be for evaluating variants in the human genome). I am familiar with the Human Splicing Finder, but am looking to try others. Open-source would be ideal, and if possible something that can be scripted into a workflow. Thanks.
A review of some potentially relevant tools, databases, algorithms, etc. can be found in Table 1.2 on page 52-53 of this thesis.
Also this post is highly relevant: Alternative splicing detection
This is the one I've used for a while, but its quite old:
Can't say I have any hard evidence of its accuracy, but it's easy to use. But I don't see how to incorporate it into a script
Hi Alex, sorry if this reply is a bit late.
I have used Human Splicing Finder and GeneSplicer but I would recommend AspAlt (Alternative-splicing and Alternative Transcription) tool along with EuSplice.
Unfortunately, these are not open-source but the accuracy is impressive. They follow a scoring system for predicted cryptic splice sites and compare them with known splice junctions which I found useful. Again this is only my opinion, comments welcome!
you can use maxent 5'ss or maxent 3'ss to evaluate them. a former post-doc in my lab (before i joined) developed it. the model gives you a splice site strength in units of bits, where higher values correspond to better splice sites. values below 0 tend to be annotation errors or have something weird going on. bits are additive, so you can subtract the variant's score from that of the consensus to determine the expected effect on splicing.
note that maxent does not accurately model u12 (ATAC) introns.
I just came over here to ask the same question with a focus on tools for plant RNA splice site prediction... Due to my best knowledge genesplicer (Pertea et al., 2001) is the latest available tool for A. thaliana. Another one is from the Brunak group: NetGene2 (Hebsgaard et al., 1996). I can't believe that there wasn't any progress in this field for the last five to ten years?